Well, in my games magic never replaced the rogue either. But that was only because I consciously put in stuff for him to do _and_ the other players decided not to make him obsolete by stepping on his toes.In my games magic never replaced the rogue. Sure, it can do what a rogue does but a rogue does it better with less resources spent.
They had no trouble at all, though, to make up for his absence when he couldn't make it to a session.
The spell system does a _very_ good job of marginalizing the skill system in 3E.